How to download from the PDB/snapshot archive

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PDB Archive

The PDB data sites are updated every Wednesday at 00:00 UTC / 09:00 JST.
( The PDB NextGen Repositories are updated every month on the 1st Wednesday at 00:00 UTC / 09:00 JST.)

The latest PDB raw data is available from the PDB Archive site.

The available protocols are https, ftp, and rsync.
There are two types of our archive site: the data archive (data.pdbjlc1.pdbj.org) that includes the latest PDBj data and the wwPDB archives (split into files.pdbj.org , files-versioned.pdbj.org and files-nextgen.pdbj.org).
The PDB archive provided by PDBj is a superset of the wwPDB data, including the original wwPDB data; core , versioned , nextgen, and our own generated data and archives.

Archives	Protocols
Archives	https	ftp	rsync
wwPDB core Archives@PDBj	https://files.pdbj.org/	ftp://ftp.pdbj.org/	rsync -az rsync.pdbj.org::
wwPDB Versioned Archive@PDBj	https://files-versioned.pdbj.org/	ftp://ftp-versioned.pdbj.org/	rsync -az rsync-versioned.pdbj.org::
wwPDB next generation Archive@PDBj	https://files-nextgen.pdbj.org/	ftp://ftp-nextgen.pdbj.org/	rsync -az rsync-nextgen.pdbj.org::
PDBj data Archive (including wwPDB Archives)	https://data.pdbjlc1.pdbj.org/	ftp://data.pdbjlc1.pdbj.org/	rsync -az data.pdbjlc1.pdbj.org::

Using the FTP protocol

Connect to the PDBj FTP site (ftp://data.pdbjlc1.pdbj.org/) using your prefered FTP client in PASSIVE mode.

Using the rsync protocol

This is useful for full/partial mirroring of the PDB archive. Several entry points are provided, which can be viewed using the following command:

 $ rsync data.pdbjlc1.pdbj.org::
Welcome to PDBj FTP site.

ftp               Top level of pdb data ftp tree aproximately 1.3T ( /pub/pdb )
ftp_data          Data directory within ftp archive aproximately 652G ( /pub/pdb/data )
ftp_derived       Derived data directory within ftp archive aproximately 467M ( /pub/pdb/derived_data )
ftp_doc           Doc directory within ftp archive aproximately 391M ( /pub/pdb/doc )
emdb              Top level of emdb data ftp tree aproximately 13T ( /pub/emdb )
ftp_versioned     Top level of pdb_versioned data ftp tree aproximately 237G ( /pdb_versioned )
pdb_nextgen       Top level of NextGen PDB archive tree approximately 85G ( /pdb_nextgen )
rsync             Top level of PDBj FTP tree aproximately 21T ( / )

To download the entry files in PDB format the following rsync command can be used:

rsync -avz --delete data.pdbjlc1.pdbj.org::ftp_data/structures/divided/pdb/ ./pdb

To download the entry files in PDB exchange format (mmCIF) the following rsync command can be used:

rsync -avz --delete data.pdbjlc1.pdbj.org::ftp_data/structures/divided/mmCIF/ ./mmCIF

To download the entry files in PDBML format the following rsync command can be used:

rsync -avz --delete data.pdbjlc1.pdbj.org::ftp_data/structures/divided/XML/ ./XML

To download the entry files in EMDB format the following rsync command can be used:

rsync -avz --delete data.pdbjlc1.pdbj.org::emdb/ ./emdb

Snapshot Archive

The wwPDB provides a snapshot archive that contains the snapshots of the FTP archive just before the first release every year or any remediations at the wwPDB Snapshots Archive (https://s3snapshots.rcsb.org/). We provide a mirror at ftp://snapshots.pdbj.org.

Using the FTP protocol

Connect to ftp://snapshots.pdbj.org/ using your prefered FTP client in PASSIVE mode.

Using the rsync protocol

This is useful for full/partial mirroring of the shapshot archive. Several entry points are provided, which can be viewed using the following command:

 $ rsync snapshots.pdbj.org::

all             Entire Snapshots archive
20050106        January 6, 2005 snapshot
20060103        January 3, 2006 snapshot
20070102        January 2, 2007 snapshot
20070731        July 31, 2007 snapshot
20080107        January 7, 2008 snapshot
20090105        January 5, 2009 snapshot
20090316        March 16, 2009 snapshot
20100104        January 4, 2010 snapshot
20110103        January 3, 2011 snapshot
20110707        July 7, 2011 snapshot
20120102        January 2, 2012 snapshot
20130101        January 1, 2013 snapshot
20140102        January 2, 2014 snapshot
20141203        December 3, 2014 snapshot
20150102        January 2, 2015 snapshot
20160101        January 1, 2016 snapshot
20160302        March 2, 2016 snapshot (Validation Reports Only)
20170101        January 1, 2017 snapshot
20170308        March 8, 2017 snapshot (Validation Reports Only)
20170710        July 10, 2017 snapshot
20180101        January 1, 2018 snapshot
20180321        March 21, 2018 snapshot (Validation Reports Only)
20190101        January 1, 2019 snapshot
20200101        January 1, 2020 snapshot
20200610        June 10, 2020 snapshot (Validation Reports Only)
20200722        July 22, 2020 snapshot
20200916        September 16, 2020 snapshot (Validation Reports Only)
20210105        January 5, 2021 snapshot
20220103        January 3, 2022 snapshot
20230102        January 2, 2023 snapshot
20240101        January 1, 2024 snapshot
20250101        January 1, 2025 snapshot

To download the shapshot from 2005-01-06 and put them in the 20050106_snapshot directory, the following command can be used:

rsync -a snapshots.pdbj.org::20050106 20050106_snapshot

Created: 2020-11-05 (last edited: 4 months ago)